Dear all,
I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.htm...).
All my subjects are part of the same group, so I used a FSGD with the group "main" to create the design matrix and mask for my data that are required by PALM. Having a closer look at the design matrix that was created, I found that there was a variable for the group that was the same for all my patients. As it is the same for all patients, I thought eliminating it would not be a problem. But after re-running PALM without it, there were huge differences in my results and effects were notably larger and more significant.
Do any of you have any experience which option is best in this case? Is it a valid choice to eliminate the variable for the group, as it is the same for each patient anyway?
Furthermore, would you recommend centering for the design matrix? I found that this can have an impact, but I am lost on in which cases it should be done and in which it shouldn't.
Thank you for your help!
Best regards
Kai Ohmstedt
can you send your fsgd file so that I have a better idea of what you are mentioning?
On 03/08/2018 08:39 AM, k.ohmstedt@stud.uni-heidelberg.de wrote:
Dear all,
I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.htm...).
All my subjects are part of the same group, so I used a FSGD with the group "main" to create the design matrix and mask for my data that are required by PALM. Having a closer look at the design matrix that was created, I found that there was a variable for the group that was the same for all my patients. As it is the same for all patients, I thought eliminating it would not be a problem. But after re-running PALM without it, there were huge differences in my results and effects were notably larger and more significant.
Do any of you have any experience which option is best in this case? Is it a valid choice to eliminate the variable for the group, as it is the same for each patient anyway?
Furthermore, would you recommend centering for the design matrix? I found that this can have an impact, but I am lost on in which cases it should be done and in which it shouldn't.
Thank you for your help!
Best regards
Kai Ohmstedt
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
k.ohmstedt＠stud.uni-heidelberg.de